Merge branch 'dockerizing-app-zolando' into 'dockerizing-app'

Use zolando

See merge request !40

.gitlab-ci.yml

@@ -45,6 +45,9 @@ test-style:
 
 
 test-sqlite:
+  # As testing for sqlite is only informative, we only run it for master
+  only:
+  - master
   extends: ".test"
 #  needs: ["test-pg"] # needs should be set to test-pg when cache is not working in gitlab-ci to spare network resources
   allow_failure: true # test is mostly informative, sqlite is not in the scope

README.md

@@ -39,7 +39,7 @@ date
 
 
 kubectl config use-context ippidb-dev
-POD=$(kubectl get po -lapplication=spilo,cluster-name=$(git branch --show)-postgresql --output jsonpath='{.items[0].metadata.name}'); echo $POD
+POD=$(kubectl get po -lapplication=spilo,cluster-name=$(git branch --show)-zolando-postgresql --output jsonpath='{.items[0].metadata.name}'); echo $POD
 date
 # 26 minutes
 gzip -d -c ippisite/db-django-4.0.sql.gz  | kubectl exec --stdin --tty $POD -- psql

chart/templates/deployment-postgres.yaml

@@ -14,6 +14,7 @@ spec:
     {{ .Values.postgresql.dbUser }}: []
   databases:
     {{ .Values.postgresql.dbName }}: {{ .Values.postgresql.dbUser }}
+  {{- if .Values.postgresql.preparedDatabases }}
   preparedDatabases:
     {{ .Values.postgresql.dbName }}:
       defaultUsers: false
@@ -22,12 +23,17 @@ spec:
     {{- toYaml . | nindent 8 }}
     {{- end }}
     schemas: {}
+  {{ end }}
   postgresql:
     version: {{ .Values.postgresql.version | quote }}
+    {{- with .Values.postgresql.parameters }}
+    {{- if . }}
     parameters:  # Expert section
-      shared_buffers: {{ .Values.postgresql.parameters.shared_buffers | quote }}
-      max_connections: {{ .Values.postgresql.parameters.max_connections | quote }}
-      log_statement: {{ .Values.postgresql.parameters.log_statement | quote }}
+      {{ if .shared_buffers }}shared_buffers: {{ .shared_buffers | quote }}{{ end }}
+      {{ if .max_connections }}max_connections: {{ .max_connections | quote }}{{ end }}
+      {{ if .log_statement }}log_statement: {{ .log_statement | quote }}{{ end }}
+    {{- end }}
+    {{- end }}
   volume:
     size: {{ .Values.postgresql.volume.size | quote }}
     storageClass:  {{ .Values.postgresql.volume.storageClass | quote }}

chart/values.yaml

@@ -101,9 +101,9 @@ redis:
 
 postgresqlBackend:
   bitnami:
-    enabled: true
-  zalando:
     enabled: false
+  zalando:
+    enabled: true
 
 postgresql:
   image: registry.opensource.zalan.do/acid/spilo-14
@@ -111,16 +111,16 @@ postgresql:
   teamId: ippidb
   dbUser: postgres
   dbName: postgres
-  version: 13
-  preparedDatabases:
-    extensions: {}
+  version: 14
+#  preparedDatabases:
+#    extensions: {}
   parameters:
-    shared_buffers: 512Gi
-    max_connections: 100
-    log_statement: ALL
+#    shared_buffers: 512Mi
+#    max_connections: 99
+    log_statement: none
   volume:
     size: 20Gi
-    storageClass: isilon
+    storageClass: 'isilon'
   resources:
     requests:
       memory: 2Gi

docker-compose.yaml

@@ -3,6 +3,7 @@ version: "3.4"
 services:
   db-local:
     image: postgres:14
+#    command: [ "postgres", "-c", "log_statement=all", ]
     volumes:
       - ippidb-dev-db-data:/var/lib/postgresql/data
       - ./ippisite:/code # for dev purpose only !!!

ippisite/ippidb/templates/targetcentric.html

@@ -234,7 +234,7 @@ Comparison and druggability prediction of protein-ligand binding sites from phar
                          <tbody>
                         {% for chain, cavities in infopdb0.items %}
                             {% with chaincount=forloop.counter %}
-                            {% for cavity, nearcavities in cavities.items %}
+                            {% for cavity in cavities %}
                                 {% with cavcount=forloop.counter %}
                                 <tr id="cavity_{{ cavity.id }}" class="table-light" >
                                     <th class="zui-sticky-col text-nowrap">
@@ -310,7 +310,7 @@ Comparison and druggability prediction of protein-ligand binding sites from phar
                                     <td>{{ cavity.t110_120|floatformat:1 }}</td>
                                     <td>{{ cavity.t120|floatformat:1 }}</td>
                                 </tr>
-                                {% for distance in nearcavities %}
+                                {% for distance in cavity.near_cavities %}
                                 {% if cavity == distance.cavity1 %}
                                     <tr class="collapse out collapseme{{ chaincount }}_{{ cavcount }}" style="background-color:rgb({{ distance.distance|get_zscore:avg_std|get_color }})">
                                         <th class="zui-sticky-col text-nowrap">

ippisite/ippidb/views/targetcentric.py

@@ -111,26 +111,26 @@ class PDBView(ListView):
                 pdb=context["pdb_list"][0].id
             ).select_related("protein__organism")
             for chain in listchainspdb0:
-                cavities = Cavity.objects.filter(chain=chain.id).select_related(
-                    "chain__protein__organism",
-                    "partner__chain__protein__organism",
-                    "partner__ligand",
-                    "chain__protein__organism",
-                    "partner__chain__protein__organism",
-                    "partner__ligand",
-                )
-                infochain = {}
-                for cavity in cavities:
-                    nearcavities = cavity.near_cavities.select_related(
-                        "cavity1__chain__protein__organism",
-                        "cavity1__partner__chain__protein__organism",
-                        "cavity1__partner__ligand",
-                        "cavity2__chain__protein__organism",
-                        "cavity2__partner__chain__protein__organism",
-                        "cavity2__partner__ligand",
-                    )
-                    infochain[cavity] = nearcavities
-                infopdb0[chain] = infochain
+                # cavities = Cavity.objects.filter(chain=chain.id).select_related(
+                #     "chain__protein__organism",
+                #     "partner__chain__protein__organism",
+                #     "partner__ligand",
+                #     "chain__protein__organism",
+                #     "partner__chain__protein__organism",
+                #     "partner__ligand",
+                # )
+                # infochain = {}
+                # for cavity in cavities:
+                #     nearcavities = cavity.near_cavities.select_related(
+                #         "cavity1__chain__protein__organism",
+                #         "cavity1__partner__chain__protein__organism",
+                #         "cavity1__partner__ligand",
+                #         "cavity2__chain__protein__organism",
+                #         "cavity2__partner__chain__protein__organism",
+                #         "cavity2__partner__ligand",
+                #     )
+                #     infochain[cavity] = nearcavities
+                infopdb0[chain] = Cavity.objects.filter(chain=chain.id)
         context["infopdb0"] = infopdb0
         completionlistpdb = list(
             PDB.objects.all().values_list("code", flat=True).distinct()